Last Updated (YYYY-MM-DD): 2019-08-06

Summary:

This is a basic and standard analysis performed on the data for this study in the HCA DCP on the above date. This analysis is intended to allow you to explore the data, as it is, in the DCP to better understand if it will be useful in your analysis. The data is not batch affect corrected but shows you signal generally in the data to allow you to explore biological and technical effects in the data as you would receive it. The original data may have been updated since last we processed the data.

Click Explore to interact and query the data (click on "view options" to explore different ordinations and metadata).

Click Download to download the data used in this portal.

Analysis Performed:

Analysis was performed from a count matrix to define the t-SNE, UMAP, and cluster labels. All metadata were collected or generated by the HCA DCP.

Original Data:

The original study can be found at https://data.humancellatlas.org/explore/projects/c4077b3c-5c98-4d26-a614-246d12c2e5d7. The original downloaded loom file can be found in the "Downloads" tab.

Publication:

"Lung, spleen and oesophagus tissue remains stable for scRNAseq in cold preservation" can be found at https://www.biorxiv.org/content/10.1101/741405v1 . The analysis in this study is a basic and standardized view of the data. Analysis in this publication should be considered authoritative when differing from this routine analysis.

Acknowledgments:

HCA data release policy can be found here. Contacts for this data are:

Elo Madissoon (em17@sanger.ac.uk), Tracey Andrew (ta11@sanger.ac.uk), Oliver Stegle (stegle@ebi.ac.uk), Kerstin B Meyer (km16@sanger.ac.uk), Anna Wilbrey-Clark (aw24@sanger.ac.uk)

Contributors include:

Emily Relton, Kourosh Saeb-Parsy, Ricardo J Miragaia, John R Ferdinand, Krishnaa Mahbubani, Anthi Tsingene, Rebecca Fitzgerald, Kevin Loudon, Nikitas Georgakopoulos, Krzysztof Polanski, Michael JT Stubbington, Ni Huang, Sarah A Teichmann, Liam Bolt, Karol Nowicki-Osuch, Phillipa Harding

HCA DCP Curators include:

Danielle Welter, Mallory Ann Freeberg, Marion F Shadbolt, Zinaida A Perova

Questions? 

Please reach out to scp-support@broadinstitute.zendesk.com